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nf-core/viralrecon: nf-core/viralrecon v2.0 - Silver Ferret

Harshil Patel; Sarai Varona; Sara Monzón; Jose Espinosa-Carrasco; Michael L Heuer; Gisela Gabernet; MiguelJulia; Phil Ewels; Stephen Kelly; Katrin Sameith; Maxime U. Garcia; jcurado

[2.0] - 2021-05-13 :warning: Major enhancements

  • Pipeline has been re-implemented in Nextflow DSL2
  • All software containers are now exclusively obtained from Biocontainers
  • Updated minimum Nextflow version to v21.04.0 (see nextflow#572)
  • BCFtools and iVar will be run by default for Illumina metagenomics and amplicon data, respectively. However, this behaviour can be customised with the --callers parameter.
  • Variant graph processes to call variants relative to the reference genome directly from de novo assemblies have been deprecated and removed
  • Variant calling with Varscan 2 has been deprecated and removed due to licensing restrictions
  • New tools:
    • Pangolin for lineage analysis
    • Nextclade for clade assignment, mutation calling and consensus sequence quality checks
    • ASCIIGenome for individual variant screenshots with annotation tracks
Other enhancements & fixes
  • Illumina and Nanopore runs containing the same 48 samples sequenced on both platforms have been uploaded to the nf-core AWS account for full-sized tests on release
  • Initial implementation of a standardised samplesheet JSON schema to use with user interfaces and for validation
  • Default human --kraken2_db link has been changed from Zenodo to an AWS S3 bucket for more reliable downloads
  • Updated pipeline template to nf-core/tools 1.14
  • Optimise MultiQC configuration and input files for faster run-time on huge sample numbers
  • [#122] - Single SPAdes command to rule them all
  • [#138] - Problem masking the consensus sequence
  • [#142] - Unknown method invocation toBytes on String type
  • [#169] - ggplot2 error when generating mosdepth amplicon plot with Swift v2 primers
  • [#170] - ivar trimming of Swift libraries new offset feature
  • [#175] - MultiQC report does not include all the metrics
  • [#188] - Add and fix EditorConfig linting in entire pipeline
Parameters Old parameter New parameter --amplicon_bed --primer_bed --amplicon_fasta --primer_fasta --amplicon_left_suffix --primer_left_suffix --amplicon_right_suffix --primer_right_suffix --filter_dups --filter_duplicates --skip_adapter_trimming --skip_fastp --skip_amplicon_trimming --skip_cutadapt --artic_minion_aligner --artic_minion_caller --artic_minion_medaka_model --asciigenome_read_depth --asciigenome_window_size --blast_db --enable_conda --fast5_dir --fastq_dir --ivar_trim_offset --kraken2_assembly_host_filter --kraken2_variants_host_filter --min_barcode_reads --min_guppyplex_reads --multiqc_title --platform --primer_set --primer_set_version --public_data_ids --save_trimmed_fail --save_unaligned --sequencing_summary --singularity_pull_docker_container --skip_asciigenome --skip_bandage --skip_consensus --skip_ivar_trim --skip_nanoplot --skip_pangolin --skip_pycoqc --skip_nextclade --skip_sra_fastq_download --spades_hmm --spades_mode --cut_mean_quality --filter_unmapped --ivar_trim_min_len --ivar_trim_min_qual --ivar_trim_window_width --kraken2_use_ftp --max_allele_freq --min_allele_freq --min_base_qual --min_coverage --min_trim_length --minia_kmer --mpileup_depth --name --qualified_quality_phred --save_align_intermeds --save_kraken2_fastq --save_sra_fastq --skip_sra --skip_vg --unqualified_percent_limit --varscan2_strand_filter

NB: Parameter has been updated if both old and new parameter information is present. NB: Parameter has been added if just the new parameter information is present. NB: Parameter has been removed if new parameter information isn't present.

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